The field of the invention is nucleoside analogues and methods of their use.
Nucleoside and nucleotide analogs have long been used as pharmaceutical ingredients against a variety of viruses and cancers. Currently, a number of nucleoside and nucleotide analogues are in clinical trials for several diseases.
In the cell, nucleosides and nucleotides are phosphorylated or further phosphorylated to the corresponding nucleoside triphosphates. Nucleoside triphosphates serve as inhibitors of DNA or RNA polymerases. Nucleoside triphosphates can also be incorporated into DNA or RNA, which interferes with the elongation of DNA or RNA.
Active nucleoside analogues are generally readily phosphorylated in the target cell. Corresponding nucleoside triphosphates have a high affinity to catalytic sites of the polymerases and compete with the natural nucleoside triphosphates as the substrate of the polymerases.
Certain nucleoside analogues work at the nucleoside or the monophosphate level. One group of promising nucleoside analogues is the nucleosides with conformationally locked sugar moieties. It has been reported that certain conformationally locked carbocyclic nucleoside analogues demonstrated potent activity against HCMV, HSV, and EBV (Siddiqui et al. Nucleosides Nucleotides 1996, 15, 235-250; Marquez et al. J. Med. Chem. 1996, 39, 3739-3747). A conformationally locked, carbocyclic AZT 5xe2x80x2-triphosphate has been reported to be an equipotent inhibitor of HIV reverse transcriptase (Marquez et al. J. Am. Chem. Soc. 1998, 120, 2780-2789). Other nucleosides with bicyclic sugar moieties were also prepared even though no activity was found or reported (Chao et al. Tetrahedron 1997, 53, 1957-1970; Okabe et al. Tetrahedron lett. 1989, 30, 2203-2206, Hong, et al. Tetrahedron Lett. 1998, 39, 225-228).
Favorable, conformationally locked nucleosides are expected to have a positive impact on antisense oligonucleotides. Oligonucleotides, as potential antisense therapeutics, have been recognized and explored for two decades. Oligonucleotides are capable of forming a double or triple helix with complementary DNA or RNA and have the ability to target the specific sequences in the viral and cancer genome. Specific binding of oligonucleotides to the DNA or RNA targets of interest would inactivate the function associated with the DNA or RNA such as replication, transcription, and translation. Therefore, viral cycles, or cancerous processes can be interrupted while the normal cell cycles are not affected.
Since natural oligonucleotides are labile to the cellular and extracellular nucleases, a great deal of efforts has been made on the study of oligonucleotide modifications, especially those modifications aimed at improving nuclease resistance and binding affinity. Oligonucleotides containing certain bicyclic nucleosides have been shown to demonstrate improved nuclease stability (Leumann et al. Bioorg. Med. Chem. Letts. 1995, 5, 1231-4; Altmann et al. Tetrahedron Lett. 1994, 35, 2331-2334, 7625-7628). Recently, 2xe2x80x2-O, 4xe2x80x2-C-methylene ribonucleosides, which have a locked 3xe2x80x2-endo sugar pucker, were synthesized and incorporated into oligonucleotides. Hybridization studies show that conformationally locked nucleosides can significantly enhance hybridization of modified oligonucleotides to the complementary RNA and DNA (Obika et al. Tetrahedron Lett. 1997, 38, 8735-8738; Koshkin et al. Tetrahedron 1998, 54, 3607-3630).
There is a need for new, conformationally locked nucleosides with bicyclic sugar moieties. These novel nucleosides should be useful in antiviral, anti-cancer, and other therapies.
Conformationally locked bicyclic-sugar nucleosides, which have a common geometrical shape, and methods for producing conformationally locked bicyclic-sugar nucleosides are described. Nucleosides are provided having bicyclic sugar moieties and oligonucleotides comprising the following formula: 
Wherein X, Y and Z are independently selected from a group of O, S, CH2, NR, Cxe2x95x90O, Cxe2x95x90CH2 or nothing, where R is selected from a group of hydrogen, alkyl, alkenyl, alkynyl, acyl; R1 is selected from a group of adenine, cytosine, guanine, hypoxanthine, uracil, thymine, heterocycles, H, OCH3, OAc, halogen, sulfonate; R2, R3 are independently selected from a group of H, OH, DMTO, TBDMSO, BnO, THPO, AcO, BzO, OP(NiPr2)O(CH2)2CN, OPO3H, PO3H, diphosphate, triphosphate; R2 and R3 together can be PhCHO2, TIPDSO2 or DTBSO2.
The novel nucleosides described herein are anticipated to be useful in antiviral, anti-cancer, and other therapies. Oligonucleotides composed of these modified nucleosides have desired physiological stability and binding affinity that enable them to be useful in therapeutics and diagnostics.